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- PDB-5exf: Thermostable aldehyde dehydrogenase from Pyrobaculum sp.1860 comp... -

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Basic information

Entry
Database: PDB / ID: 5exf
TitleThermostable aldehyde dehydrogenase from Pyrobaculum sp.1860 complexed with NADP+
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde dehydrogenase / thermostable
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesPyrobaculum ferrireducens (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsPetrova, T. / Bezsudnova, E.Y. / Boyko, K.M. / Nikolaeva, A.Y. / Rakitina, T.V. / Popov, V.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
RSF14-24-00172 Russian Federation
CitationJournal: Archaea / Year: 2016
Title: NADP-Dependent Aldehyde Dehydrogenase from ArchaeonPyrobaculum sp.1860: Structural and Functional Features.
Authors: Bezsudnova, E.Y. / Petrova, T.E. / Artemova, N.V. / Boyko, K.M. / Shabalin, I.G. / Rakitina, T.V. / Polyakov, K.M. / Popov, V.O.
History
DepositionNov 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,71317
Polymers435,6748
Non-polymers6,0399
Water56,0093109
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,9039
Polymers217,8374
Non-polymers3,0665
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27200 Å2
ΔGint-114 kcal/mol
Surface area59850 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,8108
Polymers217,8374
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26650 Å2
ΔGint-115 kcal/mol
Surface area59980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.590, 208.720, 164.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Aldehyde dehydrogenase


Mass: 54459.207 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum ferrireducens (archaea) / Gene: P186_1147 / Plasmid: Pqe (qiagen), pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): Dlt1270/prare2 / References: UniProt: G7VCG0
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Imidazole ph 6.5, 1.2 M soduim acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→92.8 Å / Num. obs: 326817 / % possible obs: 98.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 5.3
Reflection shellResolution: 2.19→2.23 Å / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 1.7 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H73

4h73


Resolution: 2.19→90.965 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 30774 4.98 %Random selection
Rwork0.2064 ---
obs0.2083 317478 97.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→90.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30099 0 390 3109 33598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831483
X-RAY DIFFRACTIONf_angle_d1.07142837
X-RAY DIFFRACTIONf_dihedral_angle_d13.56511430
X-RAY DIFFRACTIONf_chiral_restr0.0464828
X-RAY DIFFRACTIONf_plane_restr0.0065502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.21490.375710280.332319340X-RAY DIFFRACTION96
2.2149-2.24090.36199850.318219398X-RAY DIFFRACTION96
2.2409-2.26830.34379850.314319752X-RAY DIFFRACTION97
2.2683-2.2970.35469240.310119753X-RAY DIFFRACTION98
2.297-2.32720.348410770.301719608X-RAY DIFFRACTION98
2.3272-2.35910.32289670.289119704X-RAY DIFFRACTION98
2.3591-2.39280.32910320.287819750X-RAY DIFFRACTION98
2.3928-2.42850.307710370.270619756X-RAY DIFFRACTION98
2.4285-2.46650.30439890.271319677X-RAY DIFFRACTION98
2.4665-2.50690.307710450.267319786X-RAY DIFFRACTION98
2.5069-2.55010.292410640.257619683X-RAY DIFFRACTION98
2.5501-2.59650.2969620.251219835X-RAY DIFFRACTION98
2.5965-2.64650.2899370.238619786X-RAY DIFFRACTION98
2.6465-2.70050.29659880.239219721X-RAY DIFFRACTION97
2.7005-2.75920.265811300.2319488X-RAY DIFFRACTION97
2.7592-2.82340.290110490.232419350X-RAY DIFFRACTION96
2.8234-2.8940.27529610.218519315X-RAY DIFFRACTION96
2.894-2.97230.258410740.217819579X-RAY DIFFRACTION98
2.9723-3.05970.260911610.211519725X-RAY DIFFRACTION98
3.0597-3.15850.255410510.206319745X-RAY DIFFRACTION98
3.1585-3.27140.23610750.198819808X-RAY DIFFRACTION98
3.2714-3.40240.22559930.180319807X-RAY DIFFRACTION98
3.4024-3.55720.194410060.168219740X-RAY DIFFRACTION98
3.5572-3.74480.20611000.167519670X-RAY DIFFRACTION98
3.7448-3.97940.195811570.157419430X-RAY DIFFRACTION97
3.9794-4.28670.18029260.14518953X-RAY DIFFRACTION94
4.2867-4.7180.15869660.12719702X-RAY DIFFRACTION97
4.718-5.40070.15119710.131319639X-RAY DIFFRACTION97
5.4007-6.80390.197910210.154719441X-RAY DIFFRACTION96
6.8039-91.04330.19311130.160718705X-RAY DIFFRACTION93

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